Thesis

The development and application of routine gastrointestinal microbiome characterisation in the laboratory mouse using next generation sequencing

Creator
Rights statement
Awarding institution
  • University of Strathclyde
Date of award
  • 2022
Thesis identifier
  • T17200
Person Identifier (Local)
  • 201561713
Qualification Level
Qualification Name
Department, School or Faculty
Abstract
  • Despite >60% of UK in vivo studies being conducted upon mice, routine characterisation of its gastrointestinal (GI) microbiome during drug discovery is not conducted despite the understanding of its role in the health of the host. Outsourced 16S rRNA gene-based experiments were conducted to develop an ethical sampling strategy by assessing diversity along the GI tract, the effect of transport, and sex bias. The diversity of excreted faeces was identical to colonic digesta, while the stomach was highly populated in contrast to the small intestine in both sexes. During transit from a commercial supplier 29% of operational taxonomic units (OTUs) were lost from the GI tract, which was shown to last >3-months in subsequent analysis. A comparison of GI diversity using 16S rRNA gene analysis, DNA metagenomics, and RNA-seq was conducted using the MG-RAST analysis server. No taxonomic agreement was evident between methods or databases while slow processing deterred further use. An in-house, hybrid, species-level method of characterising the 16S rRNA gene was then developed by coupling the freely accessible RefSeq database and licenced Lasergene alignment software. This enabled the improved illustration of the effect of disease progression upon prokaryotic communities in both dextran sulfate sodium (DSS) and CD4+ adoptive transfer mouse models of irritable bowel disease (IBD). DSS transiently effected a range of prokaryotes in a dose dependant manner, while the GI microbiome of immunocompromised mice remained unaffected by both transport and the inflammatory response initiated by CD4+ transfer. Using this evaluative tool has increased the scope of routine health monitoring and the understanding of induced disease progression in the laboratory mouse.
Advisor / supervisor
  • Hoskisson, Paul Alan
  • Clements, Peter
Resource Type
Note
  • Previously held under moratorium in Chemistry Department (GSK) from 12th January 2023 to 28th January 2025.
DOI
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